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Over at numpy/numpy#16938 we recieved feedback where, bottom line, building a c-extension with "cython + newest numpy" broke a workflow. I wonder if there would be a way for cibuildwheel to recommend …
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Hi everyone!
I recently tried `ms2pip 3.6.3` which i have installed via `pip` and want to provide some thoughts:
While running `ms2pip --help` the argument `-m` is present (in 3e865c1 ) which …
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Hi all,
Thanks for the great tool!
I'd like to know if its currently possible to import ms2pip in a python script or the console, run the predictions and get the results in form of a pandas datafr…
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I am trying to analyze my mass spec data for the presence of small proteins. I started by searching my mgf files against Uniprot annotated and reviewed proteins. I then take the unmatched spectra and …
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Hi,
I am new to mass spec analysis and would like to use MS2PIP to improve protein predictions. My main goal is to identify small proteins in a mass spec dataset.
Currently, what I have done is…
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Hello,
I tried to use DeepLC 0.1.17 for predicting retention times for some peptides in a csv file. I also provided a calibration file to the software. When looking at the console output, I could …
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The `spec_id` column is not used in the final `spectronaut_df` dataframe that gets written.
This causes issues with some tools such as OpenSwathWorkflow that seem to require a protein ID column. Ge…
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Hi,
I'm taking a look at the config.txt file example in the repository here, and I noticed that all ptms have this opt parameter in between the mass shift and the AA residue regardless of whether …
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When I run MS2PIP locally (precompiled MS2PIP release v20190624) I regularly get C memory errors. The specific errors can vary: malloc errors, free errors, corrupted size, unspecified SIGABRT, ...
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The outputs from Elude using Linux Ubuntu (elude-v3.03) and Windows x64 (elude-v3.03) are significantly different. The output from Linux seems in line with expected iRT values (as the model was traine…